The Six Million Dollar Man (1974)
(TV Series)
After God heals Bethany, Metatron says, She can rebuld you, She has the technology. She can make you better, stronger, faster... , a reference to the "The Six Million Dollar Man".

The Breakfast Club (1985)
Jay and Silent Bob state that they were on a search for the fictional town of Shermer, Illinois, referenced in John Hughes's movies. Rufus later reveals a secret from Bethany's past about a boy named Brian Johnson, which is the same name as a character from the John Hughes film The Breakfast Club (1985) set in Shermer

Indiana Jones and the Last Crusade (1989)
Silent Bob says to a shocked passenger, after throwing the two angels off the train, "No ticket," a direct reference to Indiana Jones and the Last Crusade, when Jones throws a German officer out the window of a Zeppelin.

Clerks (1994)
The clerk at the gun store where Loki looks to purchase a weapon for his killing spree. Also, at the end of the movie, Jay suggests to go to 'Quick Stop', which is the convenience store from Clerks.

Pulp Fiction (1994)
"Well, I guess I should thank you for not sticking it up your ass."

Léon: The Professional (1994)
"And stop saying "okay" all the time. Okay?" - exact same dialogue in both 'movies'

Down to Earth (2001)
King responds to Lance after being threatened, "You gonna do something to me? I'm a friggin' angel!" In Dogma, Azreal states to Silent Bob right before getting hit with a golf club, "What are you gonna do? I'm a f**king demon!"

Indiana Jones and the Last Crusade (1989)
At about 76 minutes into the movie, Silent Bob points towards the angels he just threw off the train and says 'No Ticket'. It's a copy of when Dr Jones throws the German Officer out the window of the derigible.